Delftia tsuruhatensis, an Emergent Opportunistic Healthcare-Associated Pathogen

Complete genome sequence of Delftia tsuruhatensis strain HA60 isolated from a commercial hydroxyapatite nano-particle product (nano-hydroxyapatite)

Delftia tsuruhatensis is a Gram-negative rod-shaped aerobic bacterium with environmental remediation functions. D. tsuruhatensis strain HA60 was isolated from a commercial nano-particle product, nano-hydroxyapatite. We report that the genome of D. tsuruhatensis strain HA60 has a circular genome of 6,922,195 base pairs with a G+C content of 66.45%.

Identification of non-canonical antagonistic bacteria via interspecies contact-dependent killing

BACKGROUND

Canonical biocontrol bacteria were considered to inhibit pathogenic bacteria mainly by secreting antibiotic metabolites or enzymes. Recent studies revealed that some biocontrol bacteria can inhibit pathogenic bacteria through contact-dependent killing (CDK) mediated by contact-dependent secretion systems. The CDK was independent of antibiotic metabolites and often ignored in normal biocontrol activity assay.

RESULTS

In this study, we aimed to use a pathogen enrichment strategy to isolate non-canonical bacteria with CDK ability. Rhizosphere soil samples from Chinese cabbage showing soft rot symptom were collected and Pectobacterium carotovorum subsp. carotovorum (Pcc), the pathogen of cabbage soft rot, were added into these samples to enrich bacteria which attached on Pcc cells. By co-culture with Pcc, four bacteria strains (named as PcE1, PcE8, PcE12 and PcE13) showing antibacterial activity were isolated from Chinese cabbage rhizosphere. These four bacteria strains showed CDK abilities to different pathogenic bacteria of horticultural plants. Among them, PcE1 was identified as Chryseobacterium cucumeris. Genome sequencing showed that PcE1 genome encoded a type VI secretion system (T6SS) gene cluster. By heterologous expression, four predicted T6SS effectors of PcE1 showed antibacterial activity to Escherichia coli.

CONCLUSION

Overall, this study isolated four bacteria strains with CDK activity to various horticultural plant pathogens, and revealed possible involvement of T6SS of Chryseobacterium cucumeris in antibacterial activity. These results provide valuable insight for potential application of CDK activity in biocontrol bacteria. © 2024 Society of Chemical Industry.

Genomic analysis of multidrug-resistant Delftia tsuruhatensis isolated from raw bovine milk

Delftia tsuruhatensis is a gram-negative, aerobic bacterium mostly known as an organic pollutant degrading and growth-promoting microorganism. However, it recently emerged as an opportunistic human pathogen. To date, the source of D. tsuruhatensis infection is not clear. The majority of studies of D. tsuruhatensis have focused on environmental or clinical strains, while investigations of D. tsuruhatensis strains isolated from food sources are limited. In the present study, we report the case of D. tsuruhatensis isolation from raw bovine milk. Classical bacteriology approaches, as well as next-generation sequencing and comparative genomics, were used to characterize the features of the D. tsuruhatensis MR-6/3H strain. The MR-6/3H strain was resistant to 19 antimicrobials among 23 tested, including all aminoglycosides, phenicol, trimethoprim-sulfamethoxazole, and almost all β-lactams. Phylogenetically, the MR-6/3H was close to clinical origin strains, including those previously isolated in Russia. Comparative genomics revealed the presence of putative antimicrobial resistance genes in the MR-6/3H isolate, mostly associated with efflux systems. Notably, genus-specific OXA-926-like β-lactamase was also detected. In all, 27 putative virulence factors were predicted, the majority of which were associated with motility, adherence, stress survival, siderophore synthesis, and immunomodulation. In the MR-6/3H genome, the five prophage regions were identified, including two with intact levels. Integrons and CRISPR-Cas systems were not detected in the MR-6/3H isolate. Thus, our findings suggest that raw milk can be the potential source of and transmission route for the dissemination of multidrug-resistant D. tsuruhatensis.

Microbiome Alteration in Lung Tissues of Tuberculosis Patients Revealed by Metagenomic Next-Generation Sequencing and Immune-Related Transcriptional Profile Identified by Transcriptome Sequencing

This study explored alterations in the respiratory microbiome and transcriptome after Mycobacterium tuberculosis infection in tuberculosis (TB) patients. Metagenomic next-generation sequencing (mNGS) was adopted to reveal the microbiome in lung tissues from 110 TB and 25 nontuberculous (NonTB) patients. Transcriptome sequencing was performed in TB tissues (n = 3), tissues adjacent to TB (ParaTB, n = 3), and NonTB tissues (n = 3) to analyze differentially expressed genes (DEGs) and functional pathways. The microbial β diversity (p = 0.01325) in TB patients differed from that in the NonTB group, with 17 microbial species distinctively distributed. Eighty-three co-up-regulated DEGs were identified in the TB versus NonTB and the TB versus ParaTB comparison groups, and six were associated with immune response to Mtb. These DEGs were significantly enriched in the signaling pathways such as immune response, NF-κB, and B cell receptor. Data in the lung tissue microbiome and transcriptome in TB patients offer a sufficient understanding of the pathogenesis of TB.

Delftia tsuruhatensis TC1 symbiont suppresses malaria transmission by anopheline mosquitoes

Malaria control demands the development of a wide range of complementary strategies. We describe the properties of a naturally occurring, non-genetically modified symbiotic bacterium, Delftia tsuruhatensis TC1, which was isolated from mosquitoes incapable of sustaining the development of Plasmodium falciparum parasites. D. tsuruhatensis TC1 inhibits early stages of Plasmodium development and subsequent transmission by the Anopheles mosquito through secretion of a small-molecule inhibitor. We have identified this inhibitor to be the hydrophobic molecule harmane. We also found that, on mosquito contact, harmane penetrates the cuticle, inhibiting Plasmodium development. D. tsuruhatensis TC1 stably populates the mosquito gut, does not impose a fitness cost on the mosquito, and inhibits Plasmodium development for the mosquito's life. Contained field studies in Burkina Faso and modeling showed that D. tsuruhatensis TC1 has the potential to complement mosquito-targeted malaria transmission control.

New insights for tracking bacterial community structures in industrial wastewater from textile factories to surface water using phenotypic, 16S rRNA isolates identifications and high-throughput sequencing

Industrial wastewater can possibly change the microbial ecological environment. There are few studies that focus on the bacterial variety in textile wastewater effluents and after combination with domestic wastewater. Thus, this study aimed to determine dye degrading bacteria from textile wastewater and environmental water samples using cultural method followed by phenotypic using BIOLOG and genotypic identification (16S rRNA) for dye degrading isolates identifications. Moreover, the bacterial communities in three textile and four environmental samples using Illumina MiSeq high-throughput sequencing were investigated. The findings revealed that in textile water samples, the ratio of dye-degrading bacteria (DDB) to total bacterial counts (TBC) was 27%. The identified DDB genera by 16S rRNA based on the cultural approach were Citrobacter spp., Klebsiella spp., Enterobacter spp., Pseudomonas spp., and Aeromonas spp. Regarding to the metagenomics analyses, the environmental samples had 5,598 Operational Toxanomic Units (OTUs) more than textile wastewater samples (1,463 OTUs). Additionally, the most abundant phyla in the textile wastewater were Proteobacteria (24.45-94.83%), Bacteriodetes (0.5-44.84%) and Firmicutes (3.72-67.40%), while, Proteobacteria (30.8-76.3%), bacteroidetes (8.5-50%) and Acentobacteria (0.5-23.12%) were the most abundant phyla in the environmental samples. The maximum abundant bacteria at species level in environmental samples were Aquabacterium parvum (36.71%), Delftia tsuruhatensis (17.61%), Parabacteriodes chartae (15.39%) and Methylorubrum populi (7.51%) in El-Rahawy Drain water (RDW), River Nile water (RNW), wastewater (RWW) from WWTP in Zennin and El-Rahawy Drain sediment (RDS), respectively, whereas the maximum abundant bacteria at species level in textile wastewater were Alkalibacterium pelagium (34.11%), Enterobacter kobei (26.09%) and Chryseobacterium montanum (16.93%) in factory 1 (HBT) sample, SHB sample (before mixing with domestic wastewater) and SHB sample (after mixing with domestic wastewater), respectively. In conclusion, the microbial communities in textile wastewaters are similar to those in environmental samples at the phylum level but distinct at the genus and species levels because they are exposed to a wider range of environmental circumstances.

lactis J-12 on Hyperglycemia in Pregnancy and Pregnancy Outcomes in a High-Fat-Diet/Streptozotocin-Induced Rat Model

Bifidobacterium, a common probiotic, is widely used in the food industry. Hyperglycemia in pregnancy has become a common disease that impairs the health of the mother and can lead to adverse pregnancy outcomes, such as preeclampsia, macrosomia, fetal hyperinsulinemia, and perinatal death. Currently, Bifidobacterium has been shown to have the potential to mitigate glycolipid derangements. Therefore, the use of Bifidobacterium-based probiotics to interfere with hyperglycemia in pregnancy may be a promising therapeutic option. We aimed to determine the potential effects of Bifidobacterium animalis subsp. lactis J-12 (J-12) in high-fat diet (HFD)/streptozotocin (STZ)-induced rats with hyperglycemia in pregnancy (HIP) and respective fetuses. We observed that J-12 or insulin alone failed to significantly improve the fasting blood glucose (FBG) level and oral glucose tolerance; however, combining J-12 and insulin significantly reduced the FBG level during late pregnancy. Moreover, J-12 significantly decreased triglycerides and total cholesterol, relieved insulin and leptin resistance, activated adiponectin, and restored the morphology of the maternal pancreas and hepatic tissue of HIP-induced rats. Notably, J-12 ingestion ameliorated fetal physiological parameters and skeletal abnormalities. HIP-induced cardiac, renal, and hepatic damage in fetuses was significantly alleviated in the J-12-alone intake group, and it downregulated hippocampal mRNA expression of insulin receptor (InsR) and insulin-like growth factor-1 receptor (IGF-1R) and upregulated AKT mRNA on postnatal day 0, indicating that J-12 improved fetal neurological health. Furthermore, placental tissue damage in rats with HIP appeared to be in remission in the J-12 group. Upon exploring specific placental microbiota, we observed that J-12 affected the abundance of nine genera, positively correlating with FBG and leptin in rats and hippocampal mRNA levels of InsR and IGF-1R mRNA in the fetus, while negatively correlating with adiponectin in rats and hippocampal levels of AKT in the fetus. These results suggest that J-12 may affect the development of the fetal central nervous system by mediating placental microbiota via the regulation of maternal-related indicators. J-12 is a promising strategy for improving HIP and pregnancy outcomes.

Comparative analysis of microbial communities in different growth stages of Dermacentor nuttalli

Ticks were identified as arthropods that are pathogenic vectors. Dermacentor nuttalli is one of the dominant tick species in Inner Mongolia, and it carries and transmits a wide range of pathogenic microorganisms. However, at present, only the detection of D. nuttalli adult ticks and D. nuttalli different developmental stages carrying one specific pathogen, or the next-generation sequencing of D. nuttalli adult ticks were available. In this study, we investigated the microbial community structures of D. nuttalli in different growth stages under laboratory artificial feeding conditions. Total DNA was extracted from seven growth stages (female adult ticks, eggs, larval ticks, engorged larval ticks, nymphal ticks, engorged nymphal ticks, and second-generation adult ticks) obtained from laboratory artificial feeding of engorged D. nuttalli female ticks in Inner Mongolia. Then, the 16S rDNA V3-V4 hypervariable region was amplified to construct an Illumina PE250 library. Finally, 16S rRNA sequencing was performed on Illumina Novaseq 6000 platform. The sequencing data were analyzed using molecular biology software and platforms. The Illumina PE250 sequencing results showed that the egg stage had the highest diversity and number of species (28.74%, 98/341), while the engorged nymph stage had the lowest diversity and number of species (9.72%, 21/216). A total of 387 genera of 22 phyla were annotated in D. nuttalli, with 9 phyla and 57 genera found throughout all 7 growth stages. The dominant phylum was Proteobacteria; the dominant genera were Arsenophonus and Rickettsia; and the genera with the highest relative abundance in the 7 growth stages were Pseudomonas, Paenalcaligenes, Arsenophonus, Arsenophonus, Pseudomonas, Arsenophonus, and Rickettsia, respectively. Among the 23 exact species annotated, Brucella melitensis exhibits pathogeny that poses a serious threat to humans and animals. In this study, the microbial community composition at different growth stages of D. nuttalli was comprehensively analyzed for the first time.

The species-level microbiota of healthy eyes revealed by the integration of metataxonomics with culturomics and genome analysis

Objectives

To characterize the healthy ocular surface microbiota at the species level, including cultured and uncultured taxa.

Methods

We integrated the metataxonomic method with culturomics and genome sequencing analysis of selected isolated strains to better illustrate the taxonomic structure of the ocular surface microbiota. The metataxonomics used the full-length 16S rRNA gene sequences and the operational phylogenetic unit strategy, which can precisely identify the cultured and uncultured or potentially new taxa to species level based on the phylogenetic tree constructed.

Results

We detected 1,731 operational phylogenetic units (OPUs) in 196 healthy eyes from 128 people, affiliated to 796 cultured species, 784 potentially new species, and 151 potentially new higher taxa. The microbiota for each eye had 49.17 ± 35.66 OPUs. Of the 796 cultured species, 170 (21.36%) had previously caused clinical infections. Based on where they were initially isolated, the ocular surface microbiota mainly came from human body sites (34.55%), the environment (36.93%), plants (9.05%), animals (4.90%), and others; 428 strains were isolated from 20 eyes, affiliated to 42 species, and had come from the environment (33.33%) and the skin (16.67%). Of these, 47.62% had previously caused clinical infections. Genome analysis of 73 isolators revealed that 68.5% of them carried antibiotic resistance genes. The most frequently isolated genera, namely Staphylococcus, Streptococcus, and Moraxella, had an average of 5.30, four, and three resistance genes per strain, respectively.

Discussion

The study found that the ocular surface microbiota mainly came from the environment, plants, animals, food, and human body sites such as the skin, oral cavity, upper respiratory tract, etc. No core member of ocular surface microbiota was detected at the species level. The human eyes were invaded and colonized by bacteria from the exposed environment, some of which were capable of causing infections in humans and carried antibiotic resistance genes. Preventive measures should be developed to protect our eyes from danger.

Phylogenomic analysis of the genus Delftia reveals distinct major lineages with ecological specializations

Delftia is a diverse betaproteobacterial genus with many strains having agricultural and industrial relevance, including plant-growth promotion, bioremediation of hydrocarbon-contaminated soils, and heavy metal immobilization. Delftia spp. are broadly distributed in the environment, and have been isolated from plant hosts as well as healthy and diseased animal hosts, yet the genetic basis of this ecological versatility has not been characterized. Here, we present a phylogenomic comparison of published Delftia genomes and show that the genus is divided into two well-supported clades: one 'Delftia acidovorans' clade with isolates from soils and plant rhizospheres, and a second 'Delftia lacustris and Delftia tsuruhatensis' clade with isolates from humans and sludge. The pan-genome inferred from 61 Delftia genomes contained over 28 000 genes, of which only 884 were found in all genomes. Analysis of industrially relevant functions highlighted the ecological versatility of Delftia and supported their role as generalists.

Mycobiome Dysbiosis in Women with Intrauterine Adhesions

The vaginal microbiota dysbiosis is closely associated with the development of reproductive diseases. However, the contribution of mycobiome to intrauterine adhesion (IUA) disease remains unknown. Harnessing 16S and ITS2 rDNA sequencing analysis, we investigate both bacterial and fungal microbiota compositions across 174 samples taken from both cervical canal (CC) and middle vagina (MV) sites of IUA patients. Overall, there is no significant difference in microbial diversity between healthy subjects (HS) and IUA patients. However, we observe the IUA-specific bacterial alterations such as increased Dialister and decreased Bifidobacterium and enriched fungal genera like increased Filobasidium and Exophiala. Moreover, site-specific fungal-bacterial correlation networks are discovered in both CC and MV samples of IUA patients. Mechanistic investigation shows that Candida parapsilosis, other than Candida albicans and Candida maltosa, prevents the exacerbation of inflammatory activities and fibrosis, and modulates bacterial microbiota during IUA progression in a rat model of IUA. Our study thus highlights the importance of mycobiota in IUA progression, which may facilitate the development of therapeutic target for IUA prevention. IMPORTANCE Intrauterine adhesion (IUA) often leads to hypomenorrhea, amenorrhea, repeat miscarriages, and infertility. It has been prevalent over the last few decades in up to 13% of women who experience pregnancy termination during the first trimester, and 30% of women undergo dilation and curettage after a late, spontaneous abortion. However, the pathogenesis of IUA remains unclear. Despite reports of microbiota dysbiosis during IUA progression, there is little information on the effect of fungal microbiota on the development of IUA. This study not only enhances our understanding of the mycobiome in IUA patients but also provides potential intervention strategies for prevention of IUA by targeting mycobiome.

Metagenomic profiling of ocular surface microbiome changes in Demodex blepharitis patients

Purpose

To compare the ocular surface and meibum microbial communities of humans with Demodex Blepharitis (DB) and healthy controls.

Methods

Conjunctival sac and meibum samples from 25 DB patients and 11 healthy controls were analyzed using metagenomic next-generation sequencing (mNGS).

Results

The alpha-diversity of the conjunctival sac microbiome of the DB group (observed, Chao1, ACE) was lower than that of the control group, whereas all meibum diversity indicators were similar. In conjunctival samples, the relative abundance (RA) of the phylum Proteobacteria was significantly higher (p=0.023), and the RA of both phyla Actinobacteria and Firmicutes was significantly lower (p=0.002, 0.025, respectively) in the DB group than that in the control group. In meibum samples, the RA of the phyla Proteobacteria and Actinobacteria were similar, whereas that of the phylum Firmicutes was significantly lower in the DB group (p=0.019) than that in the control group. Linear discriminant analysis with effect size measurement of the conjunctival and meibum microbiomes showed that Sphingobium sp. YG1 and Acinetobacter guillouiae were enriched in the DB group. Sphingobium sp. YG1, Acinetobacter guillouiae and Pseudomonas putida in the DB group were related to more severe ocular surface clinical parameters. Discriminative genera’s principal coordinate analysis separated all control and DB microbiomes into two distinct clusters.

Conclusions

Proteobacteria’s increased prevalence may indicate ocular microbial community instability. The species Sphingobium sp. YG1 and Acinetobacter guillouiae are potentially pathogenic bacterial biomarkers in DB. Demodex infection mainly affects the ocular surface microbiome rather than penetrating deeper into the meibomian gland.

Two-year systematic investigation reveals alterations induced on chemical and bacteriome profile of PM2.5 by African dust incursions to the Mediterranean atmosphere

PM_2.5 atmospheric samples were regularly collected between January 2013 and March 2015 at a central location of Eastern Mediterranean (Island of Crete) during African dust events (DES) and periods of absence of such episodes as controls (CS). The elemental composition and microbiome DES and CS were thoroughly investigated. Fifty-six major and trace elements were determined by inductively coupled plasma-mass spectrometry. Relative mass abundances (RMA) of major crustal elements and lanthanoids were higher in DES than in CS. Conversely in CS, RMAs were higher for most anthropogenic transition metals. Lanthanum-to-other lanthanoids concentration ratios for DES approached the corresponding reference values for continental crust and several African dust source regions, while in CS they exceeded these values. USEPA's UNMIX receptor model, applied in all PM_2.5 samples, established that African dust is the dominant contributing source (by 80%) followed by road dust/fuel oil emissions (17%) in the receptor area. Potential source contribution function (PSCF) identified dust hotspots in Tunisia, Libya and Egypt. The application of 16S rRNA gene amplicon sequencing revealed high variation of bacterial composition and diversity between DES and CS samples. Proteobacteria, Actinobacteria and Bacteroides were the most dominant in both DES and CS samples, representing ~88% of the total bacterial diversity. Cutibacterium, Tumebacillus and Sphingomonas dominated the CS samples, while Rhizobium and Brevundimonas were the most prevalent genera in DES. Mutual exclusion/co-occurrence network analysis indicated that Sphingomonas and Chryseobacterium exhibited the highest degrees of mutual exclusion in CS, while in DES the corresponding species were Brevundimonas, Delftia, Rubellimicrobium, Flavobacterium, Blastococcus, and Pseudarthrobacter. Some of these microorganisms are emerging global opportunistic pathogens and an increase in human exposure to them as a result of environmental changes, is inevitable.

Pan-Genome Analysis of Delftia tsuruhatensis Reveals Important Traits Concerning the Genetic Diversity, Pathogenicity, and Biotechnological Properties of the Species

Delftia tsuruhatensis strains have long been known to promote plant growth and biological control. Recently, it has become an emerging opportunistic pathogen in humans. However, the genomic characteristics of the genetic diversity, pathogenicity, and biotechnological properties have not yet been comprehensively investigated. Here, a comparative pan-genome analysis was constructed. The open pan-genome with a large and flexible gene repertoire exhibited a high degree of genetic diversity. The purifying selection was the main force to drive pan-genome evolution. Significant differences were observed in the evolutionary relationship, functional enrichment, and degree of selective pressure between the different components of the pan-genome. A high degree of genetic plasticity was characterized by the determinations of diverse mobile genetic elements (MGEs), massive genomic rearrangement, and horizontal genes. Horizontal gene transfer (HGT) plays an important role in the genetic diversity of this bacterium and the formation of genomic traits. Our results revealed the occurrence of diverse virulence-related elements associated with macromolecular secretion systems, virulence factors associated with multiple nosocomial infections, and antimicrobial resistance, indicating the pathogenic potential. Lateral flagellum, T1SS, T2SS, T6SS, Tad pilus, type IV pilus, and a part of virulence-related genes exhibited general properties, whereas polar flagellum, T4SS, a part of virulence-related genes, and resistance genes presented heterogeneous properties. The pan-genome also harbors abundant genetic traits related to secondary metabolism, carbohydrate active enzymes (CAZymes), and phosphate transporter, indicating rhizosphere adaptation, plant growth promotion, and great potential uses in agriculture and biological control. This study provides comprehensive insights into this uncommon species from the genomic perspective.

IMPORTANCED. tsuruhatensis is considered a plant growth-promoting rhizobacterium (PGPR), an organic pollutant degradation strain, and an emerging opportunistic pathogen to the human. However, the genetic diversity, the evolutionary dynamics, and the genetic basis of these remarkable traits are still little known. We constructed a pan-genome analysis for D. tsuruhatensis and revealed extensive genetic diversity and genetic plasticity exhibited by open pan-genome, diverse mobile genetic elements (MGEs), genomic rearrangement, and horizontal genes. Our results highlight that horizontal gene transfer (HGT) and purifying selection are important forces in D. tsuruhatensis genetic evolution. The abundant virulence-related elements associated with macromolecular secretion systems, virulence factors, and antimicrobial resistance could contribute to the pathogenicity of this bacterium. Therefore, clinical microbiologists need to be aware of D. tsuruhatensis as an opportunistic pathogen. The genetic profiles of secondary metabolism, carbohydrate active enzymes (CAZymes), and phosphate transporter could provide insight into the genetic armory of potential applications for agriculture and biological control of D. tsuruhatensis in general.

Effect of heat stress on ileal microbial community of indigenous yellow-feather broilers based on 16S rRNA gene sequencing

Objectives

The broiler chickens are susceptible to heat stress (HS), including the indigenous broilers raised in tropical and subtropical regions. HS caused intestinal dysfunction and disrupted the gut microbiota. However, the researches about the effects of HS on ileal microbiome of indigenous broilers are limited. Therefore, this experiment used 16S rRNA sequencing to analyse the ileal microbial community in indigenous yellow‐feather broilers under HS.

Material and methods

The single factor completely random design was used in the present study, and forty 8‐week‐old Chinese indigenous yellow‐feather broilers (Huaixiang chickens) were randomly divided into two treatments: normal temperature (NT) group and HS group. There are five replications with four broilers per replicate in each group. The broilers in NT group were raised at 21.3 ± 1.2°C during the whole experimental period, the broilers in HS group were exposed to 32.5 ± 1.4°C for 8 h/day from 9:00 am to 17:00 pm and the temperature of rest time is consistent with NT group. The experiment lasted for 4 weeks.

Results

The results showed that HS exposure had no significant effects on the alpha diversity index of ileal microflora of broilers, including the Shannon, Simpson, Chao1 and ACE indexes (p > 0.05). At the genus level, HS significantly reduced the relative abundance of Campylobacter (p < 0.05), and increased the abundance of Delftia (p < 0.05). In addition, prediction of microbial community function indicated that HS significantly enhanced the abundance of the microflora related to lipid metabolism, carbohydrate metabolism and xenobiotics biodegradation and metabolism and reduced the abundance of the microflora related to nucleotide metabolism and amino acid metabolism.

Conclusions

Taken together, the present study revealed that chronic HS (4 weeks) exposure changes the abundance of the ileal microflora of broilers. These findings provided new insights into the role of HS in influencing ileal microbial community in indigenous broilers.

Detection of the Core Bacteria in Colostrum and Their Association with the Rectal Microbiota and with Milk Composition in Two Dairy Cow Farms

Simple Summary

In order to provide information on developing probiotics for newborn calves, this research detected the bacterial composition in colostrum and rectal feces of healthy Holstein cows from two dairy farms. Our results found several core bacterial species and some core genus and families in colostrum. About half of the OTUs detected in colostrum were found in the rectal content including some strictly anaerobic bacteria. In addition, some well-known intestinal beneficial bacteria including Lactobacillus plantarum and Bacillus subtilis were present in cow colostrum. Our results confirm that colostrum provides intestinal probiotics for calves. Furthermore, we might be able to develop new probiotics for calves according to the core symbiotic genus or families in colostrum.

Abstract

As one of the pioneer bacterial sources of intestinal microbiota, the information of bacterial composition in colostrum might provide a reference for developing specific probiotics for newborn calves, especially calves fed with pasteurized milk. The present study aimed to detect the core bacteria at different taxonomic levels and the common beneficial ones in colostrum by analyzing the bacterial composition in 34 colostrum samples of healthy cows selected from two dairy farms. The results of the further analysis showed that the bacterial composition in the colostrum of the two dairy farms was different, but their four most dominant phyla were the same including Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. The microbiome of all colostrum samples shared ten core operational taxonomic units (OTUs), 21 core genera, and 34 core families, and most of them had no difference in relative abundance between the two farms. The ten core OTUs did not belong to the identified commensal bacteria and have not been detected by previous study. However, several core genera found in our study were also identified as core genus in a previous study. Some well-known beneficial and pathogenic bacteria including Lactobacillus plantarum, Bacillus subtilis, Acinetobacter lwoffii, and Streptococcus pneumoniae were present in the colostrum of healthy cows. However, none had a correlation with the number of somatic cell count (SCC), but the core genera Nubella and Brevundinimas and the core families Methylobacteriaceae and Caulobacteraceae positively correlated with the number of SCC. The genus Staphylococcus, Pseudomonas, and Chryseobacterium in colostrum had a positive correlation with each other, while the probiotics unidentified-Bacteroidales-S24-7-group had a negative correlation with Pseudomonas and Chryseobacterium. In addition, more than 50% bacterial OTUs in colostrum were detected in the rectal content including some strictly anaerobic bacteria that are generally present in the intestine and rumen. However, of the top 30 commonly shared bacterial genera in the colostrum and rectal feces, no genus in colostrum was positively correlated with that same genus in rectal feces. In conclusion, the bacterial composition of colostrum microbiota is greatly influenced by external factors and individuals. There were several core OTUs, and some core genus and families in the colostrum samples. Colostrum from healthy cows contained both beneficial and pathogenic bacteria and shared many common bacteria with rectal content including some gastrointestinal anaerobes.

Genomic Analysis of Delftia tsuruhatensis Strain TR1180 Isolated From A Patient From China With In4-Like Integron-Associated Antimicrobial Resistance

Delftia tsuruhatensis has become an emerging pathogen in humans. There is scant information on the genomic characteristics of this microorganism. In this study, we determined the complete genome sequence of a clinical D. tsuruhatensis strain, TR1180, isolated from a sputum specimen of a female patient in China in 2019. Phylogenetic and average nucleotide identity analysis demonstrated that TR1180 is a member of D. tsuruhatensis. TR1180 exhibited resistance to β-lactam, aminoglycoside, tetracycline and sulphonamide antibiotics, but was susceptible to phenicols, fluoroquinolones and macrolides. Its genome is a single, circular chromosome measuring 6,711,018 bp in size. Whole-genome analysis identified 17 antibiotic resistance-related genes, which match the antimicrobial susceptibility profile of this strain, as well as 24 potential virulence factors and a number of metal resistance genes. Our data showed that Delftia possessed an open pan-genome and the genes in the core genome contributed to the pathogenicity and resistance of Delftia strains. Comparative genomics analysis of TR1180 with other publicly available genomes of Delftia showed diverse genomic features among these strains. D. tsuruhatensis TR1180 harbored a unique 38-kb genomic island flanked by a pair of 29-bp direct repeats with the insertion of a novel In4-like integron containing most of the specific antibiotic resistance genes within the genome. This study reports the findings of a fully sequenced genome from clinical D. tsuruhatensis, which provide researchers and clinicians with valuable insights into this uncommon species.

Pseudomonas aeruginosa quorum sensing inhibition by clinical isolate Delftia tsuruhatensis 11304: involvement of N-octadecanoylhomoserine lactones

Pseudomonas aeruginosa is one of the most common opportunistic pathogens that use quorum sensing (QS) system to regulate virulence factors expression and biofilm development. Delftia sp. 11304 was selected among 663 Gram-negative clinical isolates based on its QS inhibitory activity against P. aeruginosa MMA83 clinical isolate. Whole genome sequencing identified this isolate as D. tsuruhatensis and revealed genetic armamentarium of virulence factors and antibiotic resistance determinants. Ethyl acetate extract of D. tsuruhatensis 11304 culture supernatant (QSI extract) prevented biofilm formation of P. aeruginosa MMA83, but was unable to cause biofilm decomposition. QSI extract showed a synergistic effect in combination with meropenem and gentamycin, against P. aeruginosa MMA83. A dose-dependent reduction of the virulence factors: elastase, rhamnolipid and pyocyanin production by P. aeruginosa MMA83 and significant downregulation of lasI, lasR, rhlI, rhlR, pqs and mvfR expression were observed. Matrix-assisted Laser Desorption Ionization (MALDI) mass spectrometry of D. tsuruhatensis 11304 QSI extract revealed the presence of N-acyl homoserine lactones (AHL) with chain lengths of C12 to C18. The main ion peak was identified as N-octadecanoylhomoserine lactone (C₁₈-HSL). Commercial C₁₈-HSL (20 µM) reduced pyocyanin production as well as mRNA level of the lasI gene. A novel AHL species, dihydroxy-N-octadecanoylhomoserine lactone, was also described.

Delftibactin-A, a Non-ribosomal Peptide With Broad Antimicrobial Activity

The rapid emergence of drug resistant bacteria is occurring worldwide, outpacing the development of new antibiotics. It is known that some of the main sources of antibiotics are the bacteria themselves, many of which are secondary metabolites of Gram positive bacteria. Siderophores, which are secondary metabolites, function as natural chelators (e.g., iron). They are produced and secreted by many bacteria and have been experimented on as "carriers" of several types of antibiotics that pass the cell membrane of challenging Gram negative bacteria. Delftibactin A is a non-ribosomal peptide (NRP), which is known to detoxify gold in Delftia spp. and form gold nuggets, and is considered to be a siderophore. In this study we demonstrate that the supernatant from novel environmental isolates of Delftia spp. have antimicrobial activity. We characterized the active fraction and identified delftibactin A as a compound with antimicrobial activity. Delftibactin A exhibits potent antimicrobial activity against Gram positive multi drug resistant (MDR) bacteria like Methicillin-resistant Staphylococcus aureus (MRSA), and Vancomycin resistant Enterococcus (VRE), and also against the Gram negative pathogens Acinetobacter baumannii and Klebsiella pneumoniae. We discovered that the production of delftibactin A is greatly influenced by temperature. Furthermore, we have demonstrated the possibility of utilizing delftibactin A as a siderophore carrier of toxic metals such as gallium into Gram negative bacteria. These findings expose new opportunities of yet unexploited natural products such as delftibactin A, which have been known for other bacterial uses, as potent factors in the battle against MDR bacteria.

Delftia acidovorans pneumonia with lung cavities formation

Case Description

A 52-year-old female patient was admitted to our clinic with complaints of cough, sputum, fever and fatigue. The patient has been receiving immunosuppressive therapy for thrombocytopenic purpura for 5 years.

Clinical Finding

Inspiratory crackles were heard on both hemithorax. Oxygen saturation measured with the pulse oximeter was 97%. Chest X-ray showed diffuse reticular opacities that were more prominent in the upper zones of both lungs. WBC counts were 17,600 mm³ and Platelet counts were 29,000 mm³. Thorax CT showed that there were many thin-walled cavities and millimetric nodules accompanied by ground-glass infiltrates in the upper and middle lobes. Gram staining of bronchial fluid, taken by bronchoscopy, revealed Gram-negative bacilli and intense polymorphonuclear leukocytes. The bacteria were defined as Delftia acidovorans by BD Phoenix automated system.

Treatment and outcomes

The patient was hospitalized with suspicion of opportunistic pulmonary infections and cavitary lung disease. After the empirical treatment of intravenous piperacillin-tazobactam and oral clarithromycin, her clinical and radiological findings significantly regressed, and she was discharged with outpatient follow-up.

Clinical Relevance

This is the first example of cavitary pneumonia due to Delftia acidovorans in an immunocompromised patient. We would like to emphasize that Delftia pneumonia should be considered in the differential diagnosis of pulmonary cavitary involvement in such patients.